Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2013-2018 The plumed team
3 : (see the PEOPLE file at the root of the distribution for a list of names)
4 :
5 : See http://www.plumed.org for more information.
6 :
7 : This file is part of plumed, version 2.
8 :
9 : plumed is free software: you can redistribute it and/or modify
10 : it under the terms of the GNU Lesser General Public License as published by
11 : the Free Software Foundation, either version 3 of the License, or
12 : (at your option) any later version.
13 :
14 : plumed is distributed in the hope that it will be useful,
15 : but WITHOUT ANY WARRANTY; without even the implied warranty of
16 : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 : GNU Lesser General Public License for more details.
18 :
19 : You should have received a copy of the GNU Lesser General Public License
20 : along with plumed. If not, see <http://www.gnu.org/licenses/>.
21 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22 : #include "SingleDomainRMSD.h"
23 : #include "tools/PDB.h"
24 : #include "DRMSD.h"
25 :
26 : namespace PLMD {
27 :
28 975 : SingleDomainRMSD::SingleDomainRMSD( const ReferenceConfigurationOptions& ro ):
29 : ReferenceConfiguration(ro),
30 975 : ReferenceAtoms(ro)
31 : {
32 975 : }
33 :
34 367 : void SingleDomainRMSD::readReference( const PDB& pdb ) {
35 367 : readAtomsFromPDB( pdb );
36 367 : double wa=0, wd=0;
37 367 : for(unsigned i=0; i<pdb.size(); ++i) { wa+=align[i]; wd+=displace[i]; }
38 :
39 367 : Vector center;
40 7233 : for(unsigned i=0; i<pdb.size(); ++i) {
41 6866 : align[i]=align[i] / wa; displace[i]=displace[i] / wd;
42 6866 : center+=reference_atoms[i]*align[i];
43 : }
44 367 : for(unsigned i=0; i<pdb.size(); ++i) reference_atoms[i]-=center;
45 367 : }
46 :
47 596 : void SingleDomainRMSD::setReferenceAtoms( const std::vector<Vector>& conf, const std::vector<double>& align_in, const std::vector<double>& displace_in ) {
48 596 : reference_atoms.resize( conf.size() ); align.resize( conf.size() );
49 596 : displace.resize( conf.size() ); atom_der_index.resize( conf.size() );
50 596 : double wa=0, wd=0;
51 596 : for(unsigned i=0; i<conf.size(); ++i) { wa+=align_in[i]; wd+=displace_in[i]; }
52 :
53 596 : Vector center;
54 13753 : for(unsigned i=0; i<conf.size(); ++i) {
55 13157 : align[i]=align_in[i] / wa; displace[i]=displace_in[i] / wd;
56 13157 : center+=conf[i]*align[i]; atom_der_index[i]=i;
57 : }
58 596 : for(unsigned i=0; i<conf.size(); ++i) reference_atoms[i]=conf[i]-center;
59 596 : setupRMSDObject();
60 596 : }
61 :
62 58026 : double SingleDomainRMSD::calculate( const std::vector<Vector>& pos, const Pbc& pbc, ReferenceValuePack& myder, const bool& squared ) const {
63 58026 : return calc( pos, pbc, myder, squared );
64 : }
65 :
66 113840 : double SingleDomainRMSD::calc( const std::vector<Vector>& pos, const Pbc& pbc, const std::vector<Value*>& vals, const std::vector<double>& arg,
67 : ReferenceValuePack& myder, const bool& squared ) const {
68 : plumed_dbg_assert( vals.size()==0 && pos.size()==getNumberOfAtoms() && arg.size()==0 );
69 113840 : return calc( pos, pbc, myder, squared );
70 : }
71 :
72 2523 : }
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